Columnar cell lesions (CCLs) of the breast are recognized as putative precursor lesions of invasive carcinoma, but their management remains controversial. We therefore conducted a retrospective study on 311 CCLs, diagnosed in 4,164 14‐gauge core needle biopsies (CNB): 221 CCLs without atypia (CCL), 69 with atypia (CCL‐A), and 21 atypical ductal hyperplasias originating in CCL (ADH‐CCL). Two groups were identified: “immediate treatment” group undergoing excision within four months after the CNB diagnosis of CCL (N = 52) and the “wait‐and‐see” group followed up to 8 years (median 3.5 years, N = 259). In 7 of 31 women (22.5%, 1 CCL, 4 CCL‐A, 2 ADH‐CCL) who underwent immediate surgical excision and were initially biopsied for microcalcifications, ductal carcinoma in situ (DCIS) was present and in 2/31 women (6.5%, 1 CCL, 1 CCL‐A) invasive carcinoma. In 2/21 excisions (9.5%, 1 CCL, 1 CCL‐A) initially biopsied for a density, DCIS was present and invasive carcinoma in 5/21 excisions (23.8%, 2 CCL, 3 CCL‐A). In the wait‐and‐see group, 9/259 women (3.5%) developed invasive carcinoma, 6 ipsi, and 3 contralaterally. Progression risks of CCL‐A and ADH‐CCL were 18% and 22%,versus 2% for CCL without atypia (p < 0.001). In conclusion, CCL‐A or ADH‐CCL in a CNB were associated with a high risk of DCIS/invasive carcinoma in immediate surgical excision biopsies. The 8‐years progression risks for CCL‐A and ADH‐CCL were around 20%. This illustrates that an atypical CCL in a CNB may signal the presence of concurrent lesions or development of advanced lesions in future and may justify (“mini”) surgical excision.